Table 3

Top results LEO analysis, Results for top SNPs
Gene symbol M&E CGI LEO model LEO score P-value Top SNP Chr Bp Full name
BTN3A2 - Outside S → M → E 6.90 0.15 rs2093169 6 26,603,078 butyrophilin, subfamily 3, member A2
HP - Outside S → M → E 4.24 0.82 rs8044555 16 70,710,256 haptoglobin
CTSW - Outside S → M → E 2.73 0.13 rs11227306 11 65,335,248 cathepsin W
NAPRT1 - Shore S → M → E 2.69 0.11 rs4874159 8 144,742,093 nicotinate phosphoribosyltransferase domain containing 1
PHACS - Shore S → M → E 1.50 2.9e-03 rs4755227 11 44,078,659 1-aminocyclopropane-1-carboxylate synthase homolog
PNMA3 + Shore S → M → E 1.36 0.16 rs6627737 X 151,971,610 nicotinate phosphoribosyltransferase domain containing 1
CDC16 - Island S → M → E 1.09 0.01 rs11147317 13 113,957,498 cell division cycle 16 homolog (S. cerevisiae)
HRASLS3 - Shore S → E → M 2.42 7.2e-04 rs2030731 11 63,130,224 phospholipase A2, group XVI
TACSTD2 - Island S → E → M 2.08 9.5e-03 rs11207272 1 58,846,018 tumor-associated calcium signal transducer 2
SRXN1 - Shore S → E → M 1.87 5.4e-03 rs6076864 20 569,825 sulfiredoxin 1 homolog (S. cerevisiae)
C21orf56 - Outside S → E → M 1.30 2.8e-03 rs8133866 21 46,423,604 chromosome 21 open reading frame 56
BTN3A2 - Outside S → E → M 1.14 6.4e-05 rs12199613 6 26,475,197 butyrophilin, subfamily 3, member A2
WBSCR27 - Shore S → E → M 0.95 8.6e-04 rs11763011 7 72,922,084 Williams Beuren syndrome chromosome region 27
GSTM3 - Island S → E → M 0.88 1.4e-03 rs11807 1 110,062,265 glutathione S-transferase mu 3 (brain)

This table contains top probes resulting from causality analysis (LEO scores > 0.8). The top seven genes fit the causal scenario SNP → Methylation → Expression (S→M→E), while the bottom seven genes fit the reverse model in which DNA methylation is regulated by gene expression that is under genetic control (S→E→M). The Gene Symbol is given in the first column. The second column indicates whether the methylation and expression levels are associated negatively (−) or positively (+). The third column indicates whether the methylation probe is located in a CpG island (CGI), in the shore, or outside both. The columns “LEO model”, “LEO score” and “P-value” indicate which causal model fits best with the corresponding LEO score and P-value. This model fitting p-value is calculated using the model chi-square statistic statistic. The chi-square statistic tests the null hypothesis that the model is correct, thus a p-value > 0.01 indicates good fit. The next column indicates the SNP most significantly associated. The last three columns contain chromosome number and base pair location (NCBI build 36) of the SNP and full name of the gene.

van Eijk et al.

van Eijk et al. BMC Genomics 2012 13:636   doi:10.1186/1471-2164-13-636

Open Data